Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LNRM9

Calculation Name: 3P01-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P01

Chain ID: A

ChEMBL ID:

UniProt ID: Q8YLP5

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1764129.214927
FMO2-HF: Nuclear repulsion 1695515.797616
FMO2-HF: Total energy -68613.417312
FMO2-MP2: Total energy -68813.721217


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:137:GLN)


Summations of interaction energy for fragment #1(A:137:GLN)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-15.79-12.2247.147-4.517-6.1960.042
Interaction energy analysis for fragmet #1(A:137:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.091 / q_NPA : 0.045
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A139ALA00.0210.0221.996-11.750-9.3487.111-4.277-5.2360.039
4A140ALA0-0.013-0.0053.641-4.112-3.1900.037-0.224-0.7350.003
5A141GLU-1-0.762-0.8525.1870.9071.149-0.001-0.016-0.2250.000
6A142THR0-0.020-0.0146.461-0.085-0.0850.0000.0000.0000.000
7A143TYR00.0020.0067.945-0.289-0.2890.0000.0000.0000.000
8A144ASP-1-0.796-0.8779.456-0.279-0.2790.0000.0000.0000.000
9A145LEU00.0240.00611.1180.0000.0000.0000.0000.0000.000
10A146LEU0-0.018-0.00112.438-0.034-0.0340.0000.0000.0000.000
11A147LYS10.8060.89013.5830.1490.1490.0000.0000.0000.000
12A148GLN0-0.019-0.00613.790-0.064-0.0640.0000.0000.0000.000
13A149ARG10.8750.91517.102-0.272-0.2720.0000.0000.0000.000
14A150THR0-0.041-0.03217.838-0.024-0.0240.0000.0000.0000.000
15A151GLU-1-0.751-0.82020.240-0.068-0.0680.0000.0000.0000.000
16A152GLU-1-0.833-0.90920.2130.1450.1450.0000.0000.0000.000
17A153LEU0-0.0030.00122.8090.0000.0000.0000.0000.0000.000
18A154ARG10.8700.91124.3570.0560.0560.0000.0000.0000.000
19A155ARG10.8570.91322.7930.0080.0080.0000.0000.0000.000
20A156ALA0-0.0070.00127.4270.0000.0000.0000.0000.0000.000
21A157ASN00.000-0.01327.6310.0060.0060.0000.0000.0000.000
22A158ALA00.0040.01030.376-0.003-0.0030.0000.0000.0000.000
23A159GLN00.014-0.00130.798-0.001-0.0010.0000.0000.0000.000
24A160MET00.0080.00433.270-0.001-0.0010.0000.0000.0000.000
25A161SER00.0000.01434.538-0.002-0.0020.0000.0000.0000.000
26A162LEU00.0040.01836.335-0.001-0.0010.0000.0000.0000.000
27A163LEU00.0230.00037.0160.0010.0010.0000.0000.0000.000
28A164THR0-0.046-0.03537.9590.0020.0020.0000.0000.0000.000
29A165VAL00.0150.00940.100-0.001-0.0010.0000.0000.0000.000
30A166LEU00.0140.01242.271-0.001-0.0010.0000.0000.0000.000
31A167VAL00.0020.01743.7510.0000.0000.0000.0000.0000.000
32A168GLN0-0.034-0.02842.148-0.002-0.0020.0000.0000.0000.000
33A169VAL00.0180.00646.310-0.001-0.0010.0000.0000.0000.000
34A170THR0-0.024-0.02548.1960.0000.0000.0000.0000.0000.000
35A171GLN0-0.056-0.03248.853-0.001-0.0010.0000.0000.0000.000
36A172ALA0-0.0150.00650.4580.0000.0000.0000.0000.0000.000
37A173SER0-0.039-0.02252.215-0.002-0.0020.0000.0000.0000.000
38A174ASN0-0.061-0.04254.4820.0020.0020.0000.0000.0000.000
39A175SER0-0.035-0.03657.6690.0000.0000.0000.0000.0000.000
40A176LEU00.0210.00756.5520.0000.0000.0000.0000.0000.000
41A177GLU-1-0.854-0.91956.309-0.004-0.0040.0000.0000.0000.000
42A178ALA0-0.037-0.01156.094-0.002-0.0020.0000.0000.0000.000
43A179ILE00.0150.02250.676-0.002-0.0020.0000.0000.0000.000
44A180LEU0-0.0100.00451.014-0.001-0.0010.0000.0000.0000.000
45A181THR00.0660.01850.3100.0000.0000.0000.0000.0000.000
46A182PRO0-0.0090.01248.451-0.002-0.0020.0000.0000.0000.000
47A183ILE00.0270.02046.324-0.001-0.0010.0000.0000.0000.000
48A184ALA00.0150.00445.3670.0000.0000.0000.0000.0000.000
49A185THR0-0.004-0.01944.530-0.003-0.0030.0000.0000.0000.000
50A186ALA0-0.0150.00042.373-0.003-0.0030.0000.0000.0000.000
51A187PHE00.007-0.01040.6880.0000.0000.0000.0000.0000.000
52A188ALA00.015-0.00140.083-0.002-0.0020.0000.0000.0000.000
53A189GLU-1-0.860-0.90738.786-0.053-0.0530.0000.0000.0000.000
54A190SER0-0.076-0.05136.311-0.003-0.0030.0000.0000.0000.000
55A191PHE0-0.056-0.03035.3240.0020.0020.0000.0000.0000.000
56A192ALA0-0.0060.00235.196-0.002-0.0020.0000.0000.0000.000
57A193VAL0-0.0440.01537.150-0.003-0.0030.0000.0000.0000.000
58A194ASN00.0170.02140.241-0.006-0.0060.0000.0000.0000.000
59A195ALA0-0.005-0.00842.6790.0000.0000.0000.0000.0000.000
60A196CYS0-0.062-0.02144.1840.0020.0020.0000.0000.0000.000
61A197ILE00.0150.00846.115-0.001-0.0010.0000.0000.0000.000
62A198LEU0-0.0040.01649.1300.0020.0020.0000.0000.0000.000
63A199GLN0-0.003-0.01550.634-0.002-0.0020.0000.0000.0000.000
64A200MET00.0080.00853.2590.0020.0020.0000.0000.0000.000
65A201LEU0-0.013-0.00354.560-0.001-0.0010.0000.0000.0000.000
66A202GLU-1-0.840-0.89158.225-0.001-0.0010.0000.0000.0000.000
67A203GLY0-0.005-0.00861.7810.0000.0000.0000.0000.0000.000
68A204GLN0-0.031-0.02958.8310.0010.0010.0000.0000.0000.000
69A205THR0-0.0240.00559.085-0.001-0.0010.0000.0000.0000.000
70A206LEU0-0.010-0.00254.5240.0000.0000.0000.0000.0000.000
71A207SER0-0.032-0.03058.528-0.001-0.0010.0000.0000.0000.000
72A208THR0-0.005-0.00659.251-0.002-0.0020.0000.0000.0000.000
73A209ILE0-0.0060.00557.859-0.002-0.0020.0000.0000.0000.000
74A210GLN0-0.013-0.01954.7140.0000.0000.0000.0000.0000.000
75A211GLY00.0270.01053.0330.0000.0000.0000.0000.0000.000
76A212PHE0-0.038-0.02849.7300.0010.0010.0000.0000.0000.000
77A213TYR0-0.032-0.03842.4290.0000.0000.0000.0000.0000.000
78A214SER0-0.016-0.02146.5720.0010.0010.0000.0000.0000.000
79A215GLN0-0.002-0.00339.603-0.004-0.0040.0000.0000.0000.000
80A216GLN0-0.036-0.01045.297-0.003-0.0030.0000.0000.0000.000
81A217GLY00.0000.00048.4230.0010.0010.0000.0000.0000.000
82A218THR0-0.062-0.04651.4890.0020.0020.0000.0000.0000.000
83A219VAL00.0240.02250.632-0.002-0.0020.0000.0000.0000.000
84A220ASN0-0.031-0.02552.0560.0030.0030.0000.0000.0000.000
85A221ASN0-0.027-0.03252.7540.0000.0000.0000.0000.0000.000
86A222TRP00.0240.01848.5820.0010.0010.0000.0000.0000.000
87A223LEU00.0340.01149.8370.0010.0010.0000.0000.0000.000
88A224ASN0-0.015-0.01153.7330.0010.0010.0000.0000.0000.000
89A225GLN0-0.045-0.01956.0390.0000.0000.0000.0000.0000.000
90A226ASP-1-0.708-0.80350.144-0.011-0.0110.0000.0000.0000.000
91A227PRO0-0.019-0.01251.3140.0020.0020.0000.0000.0000.000
92A228LEU0-0.0120.00744.7710.0020.0020.0000.0000.0000.000
93A229THR00.016-0.02649.3650.0020.0020.0000.0000.0000.000
94A230ASN0-0.027-0.00751.0230.0020.0020.0000.0000.0000.000
95A231GLU-1-0.823-0.89548.3650.0050.0050.0000.0000.0000.000
96A232ALA00.0140.02348.4410.0020.0020.0000.0000.0000.000
97A233ILE0-0.011-0.01549.9630.0020.0020.0000.0000.0000.000
98A234ALA0-0.033-0.01353.4680.0020.0020.0000.0000.0000.000
99A235THR0-0.063-0.05849.7220.0020.0020.0000.0000.0000.000
100A236GLY0-0.029-0.00550.5560.0020.0020.0000.0000.0000.000
101A237GLN0-0.026-0.02044.6990.0020.0020.0000.0000.0000.000
102A238ILE0-0.028-0.00939.973-0.003-0.0030.0000.0000.0000.000
103A239GLN0-0.0050.00644.0880.0010.0010.0000.0000.0000.000
104A240VAL00.002-0.01438.008-0.003-0.0030.0000.0000.0000.000
105A241ALA00.0430.03540.9300.0010.0010.0000.0000.0000.000
106A242ALA00.013-0.00736.409-0.004-0.0040.0000.0000.0000.000
107A243ASN0-0.003-0.02637.174-0.005-0.0050.0000.0000.0000.000
108A244ILE00.0490.03339.8620.0030.0030.0000.0000.0000.000
109A245ALA0-0.022-0.00641.9810.0020.0020.0000.0000.0000.000
110A246LYS10.8860.93536.5960.0280.0280.0000.0000.0000.000
111A247ASP-1-0.793-0.88542.920-0.003-0.0030.0000.0000.0000.000
112A248PRO0-0.010-0.01145.426-0.002-0.0020.0000.0000.0000.000
113A249LYS10.7730.88147.594-0.001-0.0010.0000.0000.0000.000
114A250LEU0-0.014-0.01745.8250.0000.0000.0000.0000.0000.000
115A251ALA0-0.0080.00446.914-0.002-0.0020.0000.0000.0000.000
116A252SER0-0.016-0.00748.369-0.003-0.0030.0000.0000.0000.000
117A253ILE0-0.050-0.00951.3810.0000.0000.0000.0000.0000.000
118A254SER0-0.018-0.02951.820-0.001-0.0010.0000.0000.0000.000
119A255GLN00.0620.01652.634-0.003-0.0030.0000.0000.0000.000
120A256TYR0-0.013-0.02146.391-0.002-0.0020.0000.0000.0000.000
121A257GLN0-0.055-0.03348.375-0.004-0.0040.0000.0000.0000.000
122A258ASP-1-0.851-0.90249.540-0.031-0.0310.0000.0000.0000.000
123A259ASN0-0.052-0.02248.720-0.003-0.0030.0000.0000.0000.000
124A260GLY00.0180.01346.064-0.003-0.0030.0000.0000.0000.000
125A261ILE0-0.062-0.02444.157-0.003-0.0030.0000.0000.0000.000
126A262GLN0-0.003-0.01340.3430.0010.0010.0000.0000.0000.000
127A263SER0-0.045-0.02938.8480.0020.0020.0000.0000.0000.000
128A264HIS0-0.0060.01641.120-0.001-0.0010.0000.0000.0000.000
129A265VAL0-0.037-0.00838.9950.0020.0020.0000.0000.0000.000
130A266VAL00.0180.01342.436-0.002-0.0020.0000.0000.0000.000
131A267ILE00.000-0.00443.1200.0030.0030.0000.0000.0000.000
132A268PRO00.0270.02245.878-0.002-0.0020.0000.0000.0000.000
133A269ILE0-0.030-0.01747.3500.0020.0020.0000.0000.0000.000
134A270THR00.0240.00149.665-0.001-0.0010.0000.0000.0000.000
135A271TYR00.0530.04150.6130.0040.0040.0000.0000.0000.000
136A272ARG10.8620.92051.650-0.026-0.0260.0000.0000.0000.000
137A273ASN0-0.020-0.03252.3420.0030.0030.0000.0000.0000.000
138A274GLU-1-0.887-0.92554.6860.0100.0100.0000.0000.0000.000
139A275MET0-0.0110.01152.5970.0000.0000.0000.0000.0000.000
140A276LEU00.0180.00853.051-0.002-0.0020.0000.0000.0000.000
141A277GLY00.0310.00753.681-0.002-0.0020.0000.0000.0000.000
142A278VAL0-0.0260.00250.2190.0020.0020.0000.0000.0000.000
143A279LEU0-0.0020.00044.477-0.002-0.0020.0000.0000.0000.000
144A280SER0-0.012-0.01146.0490.0000.0000.0000.0000.0000.000
145A281LEU00.0170.00440.030-0.002-0.0020.0000.0000.0000.000
146A282GLN00.0570.01642.813-0.001-0.0010.0000.0000.0000.000
147A283TRP00.028-0.00437.369-0.001-0.0010.0000.0000.0000.000
148A284GLN0-0.031-0.01840.6360.0000.0000.0000.0000.0000.000
149A285GLN0-0.002-0.00436.210-0.001-0.0010.0000.0000.0000.000
150A286PRO0-0.017-0.00435.3350.0050.0050.0000.0000.0000.000
151A287ILE0-0.0140.01133.929-0.005-0.0050.0000.0000.0000.000
152A288SER0-0.037-0.03929.7210.0040.0040.0000.0000.0000.000
153A289LEU0-0.0180.01130.435-0.002-0.0020.0000.0000.0000.000
154A290ARG10.7580.83826.1730.0170.0170.0000.0000.0000.000
155A291GLU-1-0.884-0.94828.6320.0600.0600.0000.0000.0000.000
156A292ASP-1-0.817-0.87728.2050.0170.0170.0000.0000.0000.000
157A293GLU-1-0.769-0.87030.922-0.024-0.0240.0000.0000.0000.000
158A294LEU00.0180.00533.277-0.001-0.0010.0000.0000.0000.000
159A295THR0-0.034-0.02933.5660.0030.0030.0000.0000.0000.000
160A296LEU0-0.0170.00634.6030.0010.0010.0000.0000.0000.000
161A297ILE00.0090.01436.561-0.001-0.0010.0000.0000.0000.000
162A298HIS00.0310.01638.637-0.001-0.0010.0000.0000.0000.000
163A299LEU00.0000.00637.7680.0000.0000.0000.0000.0000.000
164A300SER0-0.004-0.02439.407-0.001-0.0010.0000.0000.0000.000
165A301ALA00.0240.01641.992-0.002-0.0020.0000.0000.0000.000
166A302GLN0-0.021-0.01543.2970.0010.0010.0000.0000.0000.000
167A303LEU0-0.034-0.00842.6660.0000.0000.0000.0000.0000.000
168A304VAL00.0350.01045.739-0.001-0.0010.0000.0000.0000.000
169A305ALA00.0440.02948.008-0.001-0.0010.0000.0000.0000.000
170A306ILE0-0.060-0.03148.3130.0000.0000.0000.0000.0000.000
171A307ALA00.0280.03149.117-0.001-0.0010.0000.0000.0000.000
172A308LEU00.0320.02451.144-0.001-0.0010.0000.0000.0000.000
173A309THR0-0.027-0.02953.844-0.001-0.0010.0000.0000.0000.000
174A310SER0-0.081-0.05753.5600.0000.0000.0000.0000.0000.000
175A311SER00.011-0.01954.191-0.001-0.0010.0000.0000.0000.000
176A312ARG10.8610.94256.758-0.010-0.0100.0000.0000.0000.000
177A313CYS0-0.070-0.01658.8750.0010.0010.0000.0000.0000.000
178A314SER0-0.0050.00161.192-0.001-0.0010.0000.0000.0000.000